The HugoDocs Site uses modules to integrate a theme via GitHub:

[module]
  [[module.imports]]
    path = "github.com/gohugoio/gohugoioTheme"

Is/should/will there be a way to use modules stored in a (private or team) Keybase repository?

The URL scheme is different from GitHub, GitLab etc.:

keybase://private/keybase-id/my-hugo-theme

and the Keybase software needs to run to access your (encrypted) repo.